I believe the default behavior of Safari is to open a link in the oldest open window. Minimized windows tend to get old, hence the annoyance of Safari bringing up minimized windows when opening a link from another app.
You can easily test this. Wait for it to happen. Then re-minimize the window. The behavior should be repeatable infinitely. Next copy the URL of the window you want minimized and close that window. Open a new window, paste the URL, hit return, and minimize it. Then open the external link and it will no longer go to that window.
Of course this doesn't help - it just explains the behavior. The only thing that might eventually help is filing a bug report: